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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

TODO

  • rework version to centralize it to the pyproject.toml file
  • lint
  • consider refactoring more
  • consider adding back aspera support (now available from bioconda)
  • major bump in version

Added

  • --ignore to ignore MD5 checksums

Changed

  • (BREAKING) the --force flag now overwrites existing files, but will check the MD5 checksums of the downloaded files. Previously, it would force download the file, but ignore the MD5 as well. See #21 (comment) for more details. Use the newly added --ignore flag to ignore MD5 checksums too.

2.0.4

Fixed

  • mismatch in --version output

2.0.3

Added

  • Explicit setting of SRA Lite or SRA Normalized (default) downloads
  • --sra-lite to prefer SRA Lite downloads from SRA
  • print usage on empty options

2.0.2

Added

  • --only-download-metadata to skip FASTQ downloads, and retrieve only the associated metadata @alienzj
  • fallback on SRA for metadata retrieval @gtonkinhill
  • include prefetchfor SRA downloads @gtonkinhill
  • added --force to overwrite existing downloads @gtonkinhill
  • update github actions

2.0.1

Fixed

  • Invalid fieldName(s) in ENA query @mbhall88
  • gitpod dependency and setup
  • dependabot PR

2.0.0

Added

  • Shorthand option -m for --max-attempts and -v for --verbose
  • If metadata is unavailable from ENA, try fetching metadata from SRA using pysradb
  • Provided query is validated against accession regular expressions
  • Support for Biosample/Sample accessions
  • Rich click, logging support, type hints
  • Support for Gitpod
  • Query must now be passed as --accession/-a
  • Packaging with poetry
  • README improvements

Removed

  • Deprecated --sra_only parameter is now removed
  • --ftp_only no longer required without Aspera support
  • Non-functioning --debug option
  • Uneeded logging levels

1.2.0

Fixed

  • Use accession in pigz command

Removed

  • Support for Aspera downloads
  • Manual vdb-config (no longer required in sra-tools>=3.0.1)

1.1.1

Fixed

1.1.0

Big thanks to @mbhall88 for submitting #5 with the following improvements!

Added

  • -o shorthand option for --outdir
  • a flag -F/--only-provider, which supercedes --sra_only. I left --sra_only in there for backwards compatibility and added a deprecation notice in the help description for it.
  • Conda environment file
  • Dockerfile. Feel free to try out an image from my quay.io repo here.

Changed

  • Move everything into a main function to avoid variable shadowing
  • Provider is now optional and defaults to ena. I've also made the option case insensitive, rather than listing the cased versions of the available providers
  • If ENA download fails, try SRA
  • Reduced a bunch of execute calls which were mostly operations easily dealt with by pathlib.Path
  • Changed md5sum to use hashlib.md5 instead of executing a subprocess call to md5sum
  • Moved a bunch of import statements out of function bodies to the top of the file

Removed

  • Docstring at top of file as this is a mirror of argparse's help menu and creates needless maintenance